Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange

Abstract

Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.

Keywords: Axiom 35K; array; center of diversity; couscous; domestication; durum wheat; evolution; pasta.

FIGURE 1

Statistical determination of the optimum number of clusters by discriminant analysis of principal components (DAPC).

FIGURE 2

Cluster analysis using DAPC. (A) Graphical representation of principal component 1 (IPC1) and 2 (IPC2) distances for 10 sub-populations within the whole panel. (B) Graphical representation of IPC1 and IPC2 distances for 6 sub-populations among modern germplasm.

FIGURE 3

Admixture analysis by kinship of 370 durum wheat landraces and modern elites. Each individual is represented by a horizontal line. Color codes follow the color assignment of Figure 2, with the exception of clusters 1 to 4 that were merged into one color (one cluster) when tested by STRUCTURE (light blue).

FIGURE 4

Diversity in admixture among landraces by ad hoc STRUCTURE analysis. (A) Admixture analysis by kinship color coded following the colors of Figure 2. (B) Phylogenetic tree of evolutionary distances based on kinship values color coded following the colors set in Figure 2.

FIGURE 5

Geographical distribution of the coordinate of collection of the durum wheat landraces. Color codes are provided following the colors set in Figure 2. Dashed circles indicate the two centers of origin or diversity.